Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress

Abstract

Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis–antenna proteins, plant–pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.

Biochar alleviated the toxic effects of microplastics‐contaminated geocarposphere soil on peanut (Arachis hypogaea L.) pod development: roles of pod nutrient metabolism and geocarposphere microbial modulation

“…IAA9 (P8YRGA) is the key gene in the auxin signal transduction pathway, which plays a significant role in regulating peanut pod development. 38 In the present study, the expression of IAA9 was suppressed 2.10 times in T2 compared to T1, but enhanced 5.17 times in T3 compared to T2. These results indicate that abnormal expression of key genes related to pod development in the auxin pathway caused by microplastics contamination may be an important cause of the decline in pod yield and quality, and biochar application could restore pod development by restoring the expression of key genes for pod development.…”

“…All high‐abundance DEGs of the auxin signal transduction pathway exhibited opposite expression trends in the comparisons T1‐v‐T2 and T2‐v‐T3. IAA9 ( P8YRGA ) is the key gene in the auxin signal transduction pathway, which plays a significant role in regulating peanut pod development 38 . In the present study, the expression of IAA9 was suppressed 2.10 times in T2 compared to T1, but enhanced 5.17 times in T3 compared to T2.…”

ScRNA‐seq reveals dark‐ and light‐induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L.

“…The availability of genome sequences of cultivated peanuts accelerated genomics research and breeding applications (Chen et al ., 2019 ; Zhuang et al ., 2019 ). Light and darkness serve as important environmental conditions for the development of peanut pods, which form after above‐ground fertilization with pegs extending into the soil, the latter providing dark circumstances and mechanical friction (Cui et al ., 2022 ). According to multi‐omics integration, the geocarpy was connected to gene expression involved in the gravity response, phytohormone production and phytochrome interaction factors (Chen et al ., 2016 ; Liu et al ., 2020b ; Zhang et al ., 2018 ).…”